This gene encodes a member of the 5'-3' exonuclease family. The encoded protein may be involved in replication-dependent histone mRNA degradation, and interacts directly with the enhancer of mRNA-decapping protein 4. In addition to mRNA metabolism, a similar protein in yeast has been implicated in a variety of nuclear and cytoplasmic functions, including homologous recombination, meiosis, telomere maintenance, and microtubule assembly. Mutations in this gene are associated with osteosarcoma, suggesting that the encoded protein may also play a role in bone formation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
Transcription factors with Perturb-seq knockdown data for XRN1. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = XRN1 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of XRN1, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr3:142,148,774–142,150,028 | 298.5 kb | Distal (>10kb) Multiome | 751 | |
| chr3:142,224,898–142,225,944 | 222.5 kb | Distal (>10kb) Multiome | 837 | |
| chr3:142,447,330–142,448,346 | 31 bp | At TSS Multiome | 859 | |
| chr3:142,568,423–142,569,093 | 120.6 kb | Distal (>10kb) Multiome | 163 | |
| chr3:142,578,301–142,579,268 | 130.8 kb | Distal (>10kb) Multiome | 1066 | |
| chr3:142,595,928–142,596,960 | 148.4 kb | Distal (>10kb) Multiome | 962 | |
| chr3:142,723,641–142,725,348 | 276.3 kb | Distal (>10kb) Multiome | 876 |
Genomic view of the XRN1 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.